I have an 03 R6. With the bike on a stand and I try to put in 1st or 2nd it will not go even with the engine on or off. If I rotate the rear tire a quarter turn then it will go into gear fine. What is the cause shift shaft or shift forks?

While a minor amount of movement to engage a gear is typical (see below), too much is a sign of potential issues. A little movement or a hard shift to engage a gear when not moving (and having the engine not spinning either) is typical of some gearboxes.

Motorcycles use dog engagement shift rings (unlike a car), the dogs are slightly undercut to esnure positive engagement and prevent the trans from slipping out of gear. When you rotate the tire a little bit, with the clutch in, the dog teeth can move a little and then the shift collars can be moved. This is also the reason why clutchless upshifts (and downshifts if you are mean) can be done easily on a bike...by letting off the throttle, the dogs are no longer pressed against their corresponding counterparts on the gears themselves and can then be disengaged with pressure on the shift pedal.

additional note...while in a synchomesh (car, non-racing) transmission, hard shifting will damage synchros (as the little teeth on the shift rings are fragile), while in a dog-tooth trans, hard shifting does less damage, as allowing the teeth to skip over each other is what causes damage